LAMMPS (4 May 2017)
  using 1 OpenMP thread(s) per MPI task

units           metal

atom_style      atomic
atom_modify     map array
boundary        p p p
atom_modify	sort 0 0.0

# temperature

variable t equal 1800.0

# coordination number cutoff

variable r equal 2.835

# minimization parameters

variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1

# diamond unit cell

variable a equal 5.431
lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431

region          myreg block     0 4                                 0 4                                 0 4
create_box      1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
  1 by 2 by 2 MPI processor grid
create_atoms    1 region myreg
Created 512 atoms

mass            1       28.06

group Si type 1
512 atoms in group Si

velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian

# make a vacancy

group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511

pair_style      edip/multi
pair_coeff * * Si.edip Si
Reading potential file Si.edip with DATE: 2011-09-15

thermo          10

fix             1 all nvt temp $t $t 0.1
fix             1 all nvt temp 1800 $t 0.1
fix             1 all nvt temp 1800 1800 0.1

timestep        1.0e-3
neighbor        1.0 bin
neigh_modify    every 1 delay 10 check yes

# equilibrate

run             500
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.12138
  ghost atom cutoff = 4.12138
  binsize = 2.06069, bins = 11 11 11
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair edip/multi, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1802.3816   -2372.6618            0    -2253.844    12260.967 
      10    938.75954   -2315.5185            0   -2253.6329    558.21646 
      20    534.27233   -2288.4721            0   -2253.2514    -2710.768 
      30    1043.7796   -2320.9485            0   -2252.1398    8679.4381 
      40     658.0916   -2293.8597            0   -2250.4765    2165.3742 
      50    517.93009   -2283.7238            0   -2249.5805   -1124.9373 
      60    1063.3594   -2318.4409            0   -2248.3414    7277.8526 
      70    868.14006   -2304.0134            0   -2246.7832    2050.2848 
      80    826.37805   -2300.0187            0   -2245.5416    91.099408 
      90    1289.6772   -2328.7151            0   -2243.6961    8180.7423 
     100    976.36208   -2305.9371            0   -2241.5727    3614.0499 
     110    810.81713   -2293.4705            0   -2240.0193     1359.368 
     120     1165.707   -2314.9026            0    -2238.056      7336.45 
     130    929.81245    -2297.139            0   -2235.8432    2793.8451 
     140    804.47874   -2287.2074            0    -2234.174    704.92455 
     150    1182.4141   -2310.0266            0   -2232.0787    7822.2337 
     160    979.92391   -2294.2969            0   -2229.6977    3206.7458 
     170    830.14748   -2282.6079            0   -2227.8824   -296.87377 
     180    1271.1133   -2309.4274            0   -2225.6322     7199.614 
     190    1209.6006   -2302.6407            0   -2222.9006    5528.3784 
     200    954.67693   -2283.6621            0   -2220.7273     47.02795 
     210     1260.814   -2301.5582            0    -2218.442     4829.788 
     220    1274.9954   -2299.7285            0   -2215.6774    5518.0597 
     230    1048.0074    -2282.398            0   -2213.3106    1754.4144 
     240    1261.7072   -2294.1108            0   -2210.9356    5233.2712 
     250    1272.6178   -2292.0793            0   -2208.1849    4795.9325 
     260    989.14205   -2271.0278            0   -2205.8209    -820.1828 
     270    1212.0445   -2283.4212            0     -2203.52    3395.8634 
     280    1391.9572   -2292.3809            0   -2200.6194    6666.2451 
     290    1093.1204   -2270.0421            0   -2197.9807    206.94523 
     300    1159.4831    -2272.102            0   -2195.6657    778.53806 
     310    1407.3528   -2285.6228            0   -2192.8463     5223.048 
     320    1236.7163   -2271.5389            0   -2190.0113    1865.3943 
     330    1258.8275   -2270.4611            0   -2187.4758    2333.3209 
     340    1507.9519   -2283.9906            0   -2184.5824    6775.5456 
     350    1366.5116   -2271.7287            0   -2181.6446     3432.115 
     360    1305.2829   -2265.1092            0   -2179.0614    1498.4073 
     370    1581.4335   -2280.4645            0   -2176.2122    6518.5597 
     380    1589.5319   -2277.9428            0   -2173.1567    6334.6506 
     390    1402.6781   -2262.9323            0    -2170.464    3278.3038 
     400    1374.9587   -2258.5717            0   -2167.9307    3608.7284 
     410    1295.7416   -2250.7752            0   -2165.3565    1877.5222 
     420    1278.6727   -2247.1099            0   -2162.8164    1599.4181 
     430    1508.1328   -2259.4245            0   -2160.0044    4300.2224 
     440    1624.2957   -2263.9806            0   -2156.9026     4432.625 
     450    1597.3356    -2259.263            0   -2153.9624    3370.3816 
     460    1772.0922   -2267.9106            0   -2151.0895    5788.3214 
     470    1806.4047    -2267.304            0    -2148.221    5950.1166 
     480    1593.0406   -2250.7469            0   -2145.7294    2518.0576 
     490    1660.9767    -2252.894            0    -2143.398    4282.1643 
     500     1714.283   -2253.9295            0   -2140.9194    5740.0247 
Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms

Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.16285    | 0.1688     | 0.17446    |   1.1 | 82.18
Neigh   | 0.0035172  | 0.0036234  | 0.0038214  |   0.2 |  1.76
Comm    | 0.018727   | 0.024851   | 0.030996   |   2.9 | 12.10
Output  | 0.0013061  | 0.0014012  | 0.0015635  |   0.3 |  0.68
Modify  | 0.0046582  | 0.0048603  | 0.0050988  |   0.2 |  2.37
Other   |            | 0.001861   |            |       |  0.91

Nlocal:    127.75 ave 131 max 124 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:    433.75 ave 441 max 426 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  1979.5 ave 2040 max 1895 min
Histogram: 1 0 0 0 1 0 0 0 0 2

Total # of neighbors = 7918
Ave neighs/atom = 15.4951
Neighbor list builds = 19
Dangerous builds = 0

Total wall time: 0:00:00
